SAXSdb — 3f27

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription factor SOX-17

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(DGPDTPDCPDTPDCPDTPDAPDTPDTPDGPDTPDCPDCPDTPDGPDG)-3') ; × 1 ;DNA (5'-D(DCPDCPDAPDGPDGPDAPDCPDAPDAPDTPDAPDGPDAPDGPDAPDC)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SOX17_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 5–83； UniProt 66–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3f27
Deposition date deposition_date	2008-10-29
Structure title title	Structure of Sox17 Bound to DNA
Keywords keywords	;protein-DNA complex, HMG domain, endodermal, Activator, DNA-binding, Nucleus, Transcription, Transcription regulation, Transcription-dna COMPLEX ;; Transcription/dna
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3f27__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3f27__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f27__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.85 Å
Rg (electron density)	17.13 Å
Total Rg	17.88 Å
Atom count	1283
Residues	106
Excluded volume	20695 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f27__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DGPDTPDCPDTPDCPDTPDAPDTPDTPDGPDTPDCPDCPDTPDGPDG)-3') ;
Molecular weight formula_weight	4871.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	1283

GTCTCTATTGTCCTGG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DCPDCPDAPDGPDGPDAPDCPDAPDAPDTPDAPDGPDAPDGPDAPDC)-3') ;
Molecular weight formula_weight	4925.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CCAGGACAATAGAGAC

Entity 3 Entity 3 polymer

Description description	Transcription factor SOX-17
Molecular weight formula_weight	10084.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3f27d_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

CATH v4.4 (1 domains)

Domain ID domain_id	3f27D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

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Unit-cell length a length_a	68.753 Å
Unit-cell length b length_b	68.753 Å
Unit-cell length c length_c	66.329 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.730 Å
R factor r_factor	0.2430
R_work r_work	0.2420
R_free r_free	0.2650

Structure of Sox17 Bound to DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription factor SOX-17

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3f27__assembly_1__model_1

3f27__assembly_1__model_1 | I(q)

3f27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of Sox17 Bound to DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription factor SOX-17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3f27__assembly_1__model_1

3f27__assembly_1__model_1 | I(q)

3f27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)